[BioC] gcrma background correction-saving output

Fri Dec 8 19:12:29 CET 2006

Thanks Jenny,

It solved my long term problem. I get the expected output!!

Best Regards.

Sucheta

On Fri, December 8, 2006 12:56 pm, Jenny Drnevich wrote:
> Hi Sucheta,
>
>
> 'exprs()' pulls out ALL of the probe-level values, even for MM probes and
>  the gridding probes around the edges. If you want only the PM values,
> use 'pm()'.
>
>
> Cheers,
> jenny
>
> At 10:49 AM 12/8/2006, Sucheta Tripathy wrote:
>
>> Thanks a lot Anbarasu!!
>>
>>
>> It does work. Just wanted to make sure if any values change in this
>> conversion process? My output look little srange though.
>>
>> Anyway, thanks a lot.
>>
>>
>> Sucheta
>>
>>
>> On Fri, December 8, 2006 3:55 am, Lourdusamy A Anbarasu wrote:
>>
>>> Hi,
>>>
>>>
>>>
>>> You may need to use eSet object instead of 'AffyBatch'. So, use
>>> exprs(tmp1).
>>>
>>> write.table(exprs(tmp1), file="out.txt", row.names=FALSE,
>>> col.names=FALSE, sep="\t")
>>>
>>> Hope, this helps!
>>> Anbarasu
>>>
>>>
>>>
>>> On 12/7/06, Sucheta Tripathy <sutripa at vbi.vt.edu> wrote:
>>>
>>>
>>>>
>>>> Dear List,
>>>>
>>>>
>>>>
>>>> Thanks to all who responded to my earlier question. While I can get
>>>>  going with reading multiple CEL files at a time for background
>>>> correction, I would like to save the outputs of each CEL file as a
>>>> separate text file. While I tried something like this to have the
>>>> outputs as separate columns in one file:
>>>>
>>>> library(affy) library(gcrma) affinfo=compute.affinities("soybean")
>>>> myDat <-ReadAffy()
>>>> sessionInfo()
>>>> tmp1=bg.adjust.gcrma(myDat,optical.correct=T,affinity.info=affinfo)
>>>>  write.table(tmp1, file="out.txt", row.names=FALSE,
>>>> col.names=FALSE, sep="\t")
>>>>
>>>> I get the following error
>>>>
>>>>
>>>>
>>>> Error:
>>>> -------
>>>> Error in as.data.frame.default(x[[i]], optional = TRUE) :
>>>> cannot coerce class "AffyBatch" into a data.frame
>>>>
>>>> I hope somebody can help me with this.
>>>>
>>>>
>>>>
>>>> many thanks
>>>>
>>>> Sucheta
>>>>
>>>>
>>>>
>>>> On Wed, December 6, 2006 11:57 pm, Kasper Daniel Hansen wrote:
>>>>
>>>>
>>>>> Most likely this is a bug coming from the fact that a matrix with
>>>>> 1
>>>>> row (or column) usually gets silently changed to a vector. I am
>>>>> just guessing based on the fact that it only seems to happen with
>>>>> 1 chip.
>>>>> You
>>>>> are only doing background adjusting which should work ok with only
>>>>> one chip - a full GCRMA with multichip summarization would not
>>>>> make a whole lot of sense with 1 chip.
>>>>>
>>>>> Kasper
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Dec 5, 2006, at 10:05 PM, Sucheta Tripathy wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> Hi Jean, List,
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Finally I managed to make the script
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> library(affy) library(gcrma)
>>>>>> affinfo=compute.affinities("soybean")
>>>> myDat
>>>>>> <-ReadAffy()
>>>>>> sessionInfo()
>>>>>> tmp1=bg.adjust.gcrma(myDat,optical.correct=T,affinity.info=affi
>>>>>> nfo)
>>>>>>
>>>>>>
>>>>>> run in my machine. The only thing I have noticed was it works
>>>>>> with 2
>>>>>> chips read simultaneously by ReadAffy(). For instance if I have
>>>>>> only
>>>>>>
>>>> one
>>>>>> CEL
>>>>>> file instead of 2 CEL files in the working directory then I end
>>>>>> up
>>>> having
>>>>>> the same error that I used to get before. Is there a reason for
>>>>>>  that?
>>>>>>
>>>>>> Error Message:
>>>>>> --------------
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Adjusting for optical effect.Done.
>>>>>> Computing affinities.Done.
>>>>>> Error in model.frame(formula, rownames, variables, varnames,
>>>>>> extras, extranames,  : variable lengths differ (found for 'x')
>>>>>> Execution
>>>>>> halted -----
>>>>>>
>>>>>>
>>>>>>
>>>>>> my session info: ---------------- R version 2.4.0 (2006-10-03)
>>>>>> i686-pc-linux-gnu
>>>>>>
>>>>>> locale:
>>>>>> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETA
>>>>>> RY=e
>>>>>> n_ US;LC_MESS
>>>>>> AGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C
>>>>>> ;LC_M
>>>>>> EA
>>>>>> SUREMENT=e
>>>>>> n_US;LC_IDENTIFICATION=C
>>>>>>
>>>>>> attached base packages: [1] "splines"   "tools"     "methods"
>>>>>> "stats"
>>>>>> "graphics"
>>>>>> "grDevices"
>>>>>> [7] "utils"     "datasets"  "base"
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> other attached packages: soybeanprobe   soybeancdf        gcrma
>>>>>>  matchprobes affy       affyio "1.14.0"     "1.12.0"
>>>>>> "2.7.0"
>>>>>> "1.6.0"
>>>>>> "1.12.1"      "1.0.0"
>>>>>> Biobase
>>>>>> "1.12.2"
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Sucheta
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Sucheta Tripathy, Ph.D.
>>>>>> Virginia Bioinformatics Institute Phase-I
>>>>>> Washington street.
>>>>>> Virginia Tech.
>>>>>> Blacksburg,VA 24061-0447
>>>>>> phone:(540)231-8138
>>>>>> Fax:  (540) 231-2606
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> web page: http://staff.vbi.vt.edu/sutripa blog    :
>>>>>> http://genomics-array.blogspot.com/
>>>>>> quick ref: http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/
>>>>>> R_BioCondManual.html
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioconductor mailing list
>>>>>> Bioconductor at stat.math.ethz.ch
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>> Search the archives: http://news.gmane.org/
>>>>>> gmane.science.biology.informatics.conductor
>>>>>
>>>>
>>>>
>>>> --
>>>> Sucheta Tripathy, Ph.D.
>>>> Virginia Bioinformatics Institute Phase-I
>>>> Washington street.
>>>> Virginia Tech.
>>>> Blacksburg,VA 24061-0447
>>>> phone:(540)231-8138
>>>> Fax:  (540) 231-2606
>>>>
>>>>
>>>>
>>>> web page: http://staff.vbi.vt.edu/sutripa blog    :
>>>> http://genomics-array.blogspot.com/
>>>> quick ref:
>>>> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.
>>>> html
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> Lourdusamy A Anbarasu
>>> Dipartimento Medicina Sperimentale e Sanita Pubblica
>>> Via Scalzino 3
>>> 62032 Camerino (MC)
>>>
>>>
>>>
>>
>>
>> --
>> Sucheta Tripathy, Ph.D.
>> Virginia Bioinformatics Institute Phase-I
>> Washington street.
>> Virginia Tech.
>> Blacksburg,VA 24061-0447
>> phone:(540)231-8138
>> Fax:  (540) 231-2606
>>
>>
>> web page: http://staff.vbi.vt.edu/sutripa blog    :
>> http://genomics-array.blogspot.com/
>> quick ref:
>> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
> Jenny Drnevich, Ph.D.
>
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
>
>

-- 
Sucheta Tripathy, Ph.D.
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

web page: http://staff.vbi.vt.edu/sutripa
blog    : http://genomics-array.blogspot.com/
quick ref:
http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html